{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,2]],"date-time":"2026-04-02T09:36:06Z","timestamp":1775122566217,"version":"3.50.1"},"reference-count":45,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2020,9,2]],"date-time":"2020-09-02T00:00:00Z","timestamp":1599004800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100020925","name":"Golestan University","doi-asserted-by":"crossref","award":["96-1206"],"award-info":[{"award-number":["96-1206"]}],"id":[{"id":"10.13039\/100020925","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Small molecules such as metabolites and drugs play essential roles in biological processes and pharmaceutical industry. Knowing their interactions with biomacromolecular targets demands a deep understanding of binding mechanisms. Dozens of papers have suggested that discovering of the binding event by means of conventional unbiased molecular dynamics (MD) simulation urges considerable amount of computational resources, therefore, only one who holds a cluster or a supercomputer can afford such extensive simulations. Thus, many researchers who do not own such resources are reluctant to take the benefits of running unbiased MD simulation, in full atomistic details, when studying a ligand binding pathway. Many researchers are impelled to be content with biased MD simulations which seek its validation due to its intrinsic preconceived framework. In this work, we have presented a workable stratagem to encourage everyone to perform unbiased (unguided) MD simulations, in this case a protein\u2013ligand binding process, by typical desktop computers and so achieve valuable results in nanosecond time scale. Here, we have described a dynamical binding\u2019s process of an anticancer drug, the dasatinib, to the c-Src kinase in full atomistic details for the first time, without applying any biasing force or potential which may lead the drug to artificial interactions with the protein. We have attained multiple independent binding events which occurred in the nanosecond time scales, surprisingly as little as \u223c30\u2009ns. Both the protonated and deprotonated forms of the dasatinib reached the crystallographic binding mode without having any major intermediate state during induction.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The links of the tutorial and technical documents are accessible in the article.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa565","type":"journal-article","created":{"date-parts":[[2020,6,5]],"date-time":"2020-06-05T15:27:53Z","timestamp":1591370873000},"page":"4714-4720","source":"Crossref","is-referenced-by-count":13,"title":["A boosted unbiased molecular dynamics method for predicting ligands binding mechanisms: probing the binding pathway of dasatinib to Src-kinase"],"prefix":"10.1093","volume":"36","author":[{"given":"Farzin","family":"Sohraby","sequence":"first","affiliation":[{"name":"Department of Biology, Faculty of Science, Golestan University , Gorgan 4913815759, Iran"}]},{"given":"Mostafa","family":"Javaheri Moghadam","sequence":"additional","affiliation":[{"name":"Department of Biology, Faculty of Science, Golestan University , Gorgan 4913815759, Iran"}]},{"given":"Masoud","family":"Aliyar","sequence":"additional","affiliation":[{"name":"Department of Biology, Faculty of Science, Golestan University , Gorgan 4913815759, Iran"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3745-5565","authenticated-orcid":false,"given":"Hassan","family":"Aryapour","sequence":"additional","affiliation":[{"name":"Department of Biology, Faculty of Science, Golestan University , Gorgan 4913815759, Iran"}]}],"member":"286","published-online":{"date-parts":[[2020,9,2]]},"reference":[{"key":"2023062213575133300_btaa565-B1","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1016\/j.softx.2015.06.001","article-title":"GROMACS: high performance molecular simulations through multi-level parallelism from laptops to supercomputers","volume":"1\u20132","author":"Abraham","year":"2015","journal-title":"SoftwareX"},{"key":"2023062213575133300_btaa565-B2","doi-asserted-by":"crossref","first-page":"25801","DOI":"10.1074\/jbc.M703268200","article-title":"Modulation of androgen receptor activation function 2 by testosterone and dihydrotestosterone","volume":"282","author":"Askew","year":"2007","journal-title":"J. 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